Find Mirna Targeting An Mrna Dataset

Question

[datanerd]

Hi all,

I have a list of significant mRNA and I intend to find miRNA that might be important and targeting a bunch of those mRNAs. But when I do this using all the miRNA name list from the affy, I find too many miRNAs targeting many of those mRNAs which are in common. I was looking for a way to filter this based on other criteria that could be important in the selection. Like may be prediction score?

can anyone make any suggestions on how can I do that?

Thanks In advance.

[Khader Shameer]

Which database or tool are you using ? Which organism ?

[datanerd]

Hi, Its human and I am using Targetscan. I just have the mRNA profile data and not the miRNA. But I just intent to find important miRNAs that are shared amoong my list of mRNA. Thanks!

[Khader Shameer]

Edit your question with those details, I am sure you will get better response.

Answer 1

[jlshi.nudt]

I suggest to use the GSEA tool, which can give the enrichment of miRNA for a list of gene sympols.

[datanerd]

Thanks! But i donot have miRNA profile data but just mRNA. Would you still suggest this for my query.

Answer 2

[Anthony Mathelier]

I would suggest to use different tools to predict miRNA-mRNA potential interactions and restrict yourself with the intersection. Use stringent thresholds too to be more confident. The conservation of the underlying mRNA sequence targeted is also a good criteria.

[datanerd]

Thanks! I am doing this!